Structural and mechanistic insights into prokaryotic energy-coupling factor transporters

Slotboom, Dirk Jan

doi:10.1038/nrmicro3175

Cited by 94 publications

(124 citation statements)

References 74 publications

(169 reference statements)

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“…Reorientation of BioY Loop Regions-The hypothetical toppling over mechanism (16,22,23) predicts that the S units of ECF transporters adopt an upright topology after nucleotide binding to the ATPase dimer. As a result of the ATP-induced rotation, the substrate-binding site would face the extracellular side of the membrane.…”

Section: For V(t) and F(t) C Gaussian Distance Distributions Yieldimentioning

confidence: 99%

“…The LlBioY protein had been purified and crystallized in a solitary and substrate-bound state (9). A typical feature of this structure and the structures of the substrate-loaded RibU (7) and ThiT (8) proteins is the location of the loop region connecting TMH1 and TMH2, which is predicted to face the exterior of the membrane and lies as a lid on the substrate-binding pocket (22,23). In the substrate-free holotransporter structures, the S units FolT, PdxU, and PanT are toppled over in the membrane, and this loop is orientated toward the cytoplasm.…”

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confidence: 99%

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ATP-dependent Conformational Changes Trigger Substrate Capture and Release by an ECF-type Biotin Transporter

Finkenwirth¹,

Sippach

Landmesser

et al. 2015

Journal of Biological Chemistry

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Background: Substrate-binding integral membrane proteins of ECF transporters are predicted to undergo reversible rotation during the transport cycle. Results: Capture and release of biotin by a nanodisc-embedded ECF transporter depended on ATP-induced subunit reorientations. Conclusion: ECF transporters mediate vitamin translocation by turning their substrate-specific components within the membrane. Significance: Individual steps of the transport cycle are highlighted by biochemical and biophysical techniques.

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Section: For V(t) and F(t) C Gaussian Distance Distributions Yieldimentioning

confidence: 99%

mentioning

confidence: 99%

ATP-dependent Conformational Changes Trigger Substrate Capture and Release by an ECF-type Biotin Transporter

Finkenwirth¹,

Sippach

Landmesser

et al. 2015

Journal of Biological Chemistry

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“…In contrast to other transporters that work by the rocker-switch (13) or the gated-pore (14) mechanisms, Glt Ph mediates transport by an elevator (6) mechanism in which the transport domain travels nearly 2 nm across the membrane (reviewed in ref. 15) (Fig. S1).…”

mentioning

confidence: 99%

Direct visualization of glutamate transporter elevator mechanism by high-speed AFM

Ruan

Miyagi

Wang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

107

106

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Glutamate transporters are essential for recovery of the neurotransmitter glutamate from the synaptic cleft. Crystal structures in the outward-and inward-facing conformations of a glutamate transporter homolog from archaebacterium Pyrococcus horikoshii, sodium/aspartate symporter Glt Ph , suggested the molecular basis of the transporter cycle. However, dynamic studies of the transport mechanism have been sparse and indirect. Here we present highspeed atomic force microscopy (HS-AFM) observations of membranereconstituted Glt Ph at work. HS-AFM movies provide unprecedented real-space and real-time visualization of the transport dynamics. Our results show transport mediated by large amplitude 1.85-nm "elevator" movements of the transport domains consistent with previous crystallographic and spectroscopic studies. Elevator dynamics occur in the absence and presence of sodium ions and aspartate, but stall in sodium alone, providing a direct visualization of the ion and substrate symport mechanism. We show unambiguously that individual protomers within the trimeric transporter function fully independently.Glt Ph | HS-AFM | transporter | elevator mechanism | dynamics

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“…While none of the cofactor biosynthetic pathways are present in Mycoplasma species, and thus are also lacking in M. mycoides JCVI-syn3.0, this minimal genome possesses all three general components of the so-called ECF (energy-coupling factor) transporters that are capable of transporting several cofactors (10). The substrate-specific S proteins for these transporters are generally poorly conserved and barely detectable in sequence comparisons (134,135).…”

Section: Cofactorsmentioning

confidence: 99%

The Blueprint of a Minimal Cell: MiniBacillus

Reuß

Commichau

Gundlach

et al. 2016

Microbiol Mol Biol Rev

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SUMMARYBacillus subtilisis one of the best-studied organisms. Due to the broad knowledge and annotation and the well-developed genetic system, this bacterium is an excellent starting point for genome minimization with the aim of constructing a minimal cell. We have analyzed the genome ofB. subtilisand selected all genes that are required to allow life in complex medium at 37°C. This selection is based on the known information on essential genes and functions as well as on gene and protein expression data and gene conservation. The list presented here includes 523 and 119 genes coding for proteins and RNAs, respectively. These proteins and RNAs are required for the basic functions of life in information processing (replication and chromosome maintenance, transcription, translation, protein folding, and secretion), metabolism, cell division, and the integrity of the minimal cell. The completeness of the selected metabolic pathways, reactions, and enzymes was verified by the development of a model of metabolism of the minimal cell. A comparison of theMiniBacillusgenome to the recently reported designed minimal genome ofMycoplasma mycoidesJCVI-syn3.0 indicates excellent agreement in the information-processing pathways, whereas each species has a metabolism that reflects specific evolution and adaptation. The blueprint ofMiniBacilluspresented here serves as the starting point for a successive reduction of theB. subtilisgenome.

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Structural and mechanistic insights into prokaryotic energy-coupling factor transporters

Cited by 94 publications

References 74 publications

ATP-dependent Conformational Changes Trigger Substrate Capture and Release by an ECF-type Biotin Transporter

ATP-dependent Conformational Changes Trigger Substrate Capture and Release by an ECF-type Biotin Transporter

Direct visualization of glutamate transporter elevator mechanism by high-speed AFM

The Blueprint of a Minimal Cell: MiniBacillus

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